In order to determine the impact of aflatoxin B1(AFB1) on the intestinal mucosa of Litopenaeus vannamei, shrimps were fed with normal diet and diet containing 15 mg/kg of AFB1 for 12 days, and the tissues of intestine were collected on the day 2, 4, 8 and day 12 of the experiment. The relative expression of genes in mTOR signal pathway including eif4ebp, eif4e1a, eif4e2 and p70s6k, the immune-related genes including Dorsal, Relish and proPO and mucin-like PM gene were quantified with RT-qPCR. The changes of intestinal morphology were explored under microscope. The results showed that, the expression of genes in mTOR signal pathway was affected by AFB1, eif4ebp gene was up-regulated from the 2 nd day, and decreased after reaching its peak on the 8th day; eif4e2 and eif4e1a genes were both inhibited on the 8th and 12th day; p70s6k gene was down-regulated from the 2rd to 8th day, and climbed to the initial level on the day 12. The immune response of the intestine was also stimulated by AFB1, Dorsal and Relish genes were induced significantly after fed with AFB1; proPO gene was up-regulated on the day 4 and day 8, followed by a fall to the initial level on the day 12; and the mucin-like PM gene was also significantly induced on the day 2, 4 and day 8. The morphology of shrimp gut was changed by AFB1, the nucleus of epithelial cells swelled, the clear margin of chromatin was no longer present, and the ecclasis of epithelial cell layer occurred. In conclusion, the function of intestinal mucosal barrier was affected by AFB1, not only the mechanical barrier was damaged, but also the chemical and immunologic barriers were impaired.